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- PDB-1aqz: CRYSTAL STRUCTURE OF A HIGHLY SPECIFIC ASPERGILLUS RIBOTOXIN, RES... -

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Basic information

Entry
Database: PDB / ID: 1aqz
TitleCRYSTAL STRUCTURE OF A HIGHLY SPECIFIC ASPERGILLUS RIBOTOXIN, RESTRICTOCIN
ComponentsRESTRICTOCIN
KeywordsRIBOTOXIN / RIBOSOME-INACTIVATING PROTEIN / PROTEIN-RNA SPECIFIC INTERACTION / LAUE DIFFRACTION / CELL-ENTRY ACTIVITY
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / negative regulation of translation / RNA binding / extracellular region
Similarity search - Function
Fungal ribotoxin / : / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ribonuclease mitogillin
Similarity search - Component
Biological speciesAspergillus restrictus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SINGLE ISOMORPHOUS REPLACEMENT, ANOMALOUS SCATTERING / Resolution: 1.7 Å
AuthorsYang, X. / Moffat, K.
Citation
Journal: Structure / Year: 1996
Title: Insights into specificity of cleavage and mechanism of cell entry from the crystal structure of the highly specific Aspergillus ribotoxin, restrictocin.
Authors: Yang, X. / Moffat, K.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: The Conformation of the Sarcin/Ricin Loop from 28S Ribosomal RNA
Authors: Szewczak, A.A. / Moore, P.B. / Chan, Y.L. / Wool, I.G.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Determination and Restrained Least-Squares Refinement of the Structures of Ribonuclease Sa and its Complex with 3'-Guanylic Acid at 1.8 A Resolution
Authors: Sevcik, J. / Dodson, E.J. / Dodson, G.G.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization and Preliminary Characterization of Mitogillin, a Ribosomal Ribonuclease from Aspergillus Restrictus
Authors: Martinez, S.E. / Smith, J.L.
#4: Journal: Trends Biochem.Sci. / Year: 1984
Title: The Mechanism of Action of the Cytotoxic Nuclease Alpha-Sarcin and its Use to Analyse Ribosome Structure
Authors: Wool, I.G.
#5: Journal: Nature / Year: 1982
Title: Specific Protein-Nucleic Acid Recognition in Ribonuclease T1-2'-Guanylic Acid Complex: An X-Ray Study
Authors: Heinemann, U. / Saenger, W.
History
DepositionAug 4, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RESTRICTOCIN
B: RESTRICTOCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0635
Polymers33,7782
Non-polymers2853
Water3,639202
1
A: RESTRICTOCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0793
Polymers16,8891
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RESTRICTOCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9842
Polymers16,8891
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.240, 82.160, 38.040
Angle α, β, γ (deg.)90.00, 100.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.996739, 0.022599, -0.077458), (-0.015797, -0.996054, -0.087335), (-0.079126, -0.085827, 0.993163)
Vector: 69.91313, 102.81252, -13.45481)

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Components

#1: Protein RESTRICTOCIN


Mass: 16888.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: INORGANIC PHOSPHATE GROUP AT THE ACTIVE SITE / Source: (natural) Aspergillus restrictus (mold)
References: UniProt: P67876, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46 %
Description: DATA WERE COLLECTED USING LAUE DIFFRACTION. 62 IMAGES WERE COLLECTED. TOTAL EXPOSURE TIME IS 325 MS.
Crystal growMethod: vapor diffusion, microdialysis / pH: 6.8
Details: A COMBINATION OF VAPOR DIFFUSION AND MICRODIALYSIS TECHNIQUES WERE USED TO CRYSTALLIZE RESTRICTOCIN. THE FINAL MOTHER LIQUOR CONSISTS OF 60% ETHANOL, 10MM SODIUM PHOSPHATE, PH6.8. THE ...Details: A COMBINATION OF VAPOR DIFFUSION AND MICRODIALYSIS TECHNIQUES WERE USED TO CRYSTALLIZE RESTRICTOCIN. THE FINAL MOTHER LIQUOR CONSISTS OF 60% ETHANOL, 10MM SODIUM PHOSPHATE, PH6.8. THE PROTEIN CONCENTRATION IS 10MG/ML., vapor diffusion and microdialysis
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160 %ethanol1reservoir
210 mMsodium phosphate1reservoir
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.7 / Wavelength: 0.7, 2.05
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Aug 1, 1994 / Details: MIRROR
RadiationMonochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.71
22.051
ReflectionResolution: 1.7→8 Å / Num. obs: 28328 / % possible obs: 85.6 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.039
Reflection shellResolution: 1.7→1.78 Å / % possible all: 54.8

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Processing

Software
NameVersionClassification
LaueViewdata collection
LaueViewdata reduction
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
LaueViewdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: SINGLE ISOMORPHOUS REPLACEMENT, ANOMALOUS SCATTERING
Resolution: 1.7→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.177 2232 8 %RANDOM
Rwork0.237 ---
obs0.237 28328 85.6 %-
Displacement parametersBiso mean: 19.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.18 Å
Luzzati d res low-8 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 15 205 2492
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.02
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.7→1.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.38 184 8 %
Rwork0.32 2088 -
obs--55 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.177 / Rfactor Rfree: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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